Here we perform analysis against the custom reference. The results are exported and inlcuded in the SI table.
library(tidyverse)
library(Seurat)
library(cowplot)
library(ComplexHeatmap)
library(circlize)
library(GeneOverlap)
library(gprofiler2)
library(ggrepel)
library(ggplot2)
library(muscat)
library(purrr)
library(limma)
library(scran)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.0 ✔ readr 2.1.4 ✔ forcats 1.0.0 ✔ stringr 1.5.0 ✔ ggplot2 3.4.1 ✔ tibble 3.1.8 ✔ lubridate 1.9.2 ✔ tidyr 1.3.0 ✔ purrr 1.0.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors Attaching SeuratObject Attaching package: ‘cowplot’ The following object is masked from ‘package:lubridate’: stamp Loading required package: grid ======================================== ComplexHeatmap version 2.14.0 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite either one: - Gu, Z. Complex Heatmap Visualization. iMeta 2022. - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. The new InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app with zero effort. Have a try! This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== ======================================== circlize version 0.4.15 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: https://jokergoo.github.io/circlize_book/book/ If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. This message can be suppressed by: suppressPackageStartupMessages(library(circlize)) ======================================== Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object is masked from ‘package:limma’: plotMA The following objects are masked from ‘package:lubridate’: intersect, setdiff, union The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:lubridate’: second, second<- The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:lubridate’: %within% The following objects are masked from ‘package:dplyr’: collapse, desc, slice The following object is masked from ‘package:purrr’: reduce Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Attaching package: ‘SummarizedExperiment’ The following object is masked from ‘package:SeuratObject’: Assays The following object is masked from ‘package:Seurat’: Assays Loading required package: scuttle
library(future)
#for 200gb ram
options(future.globals.maxSize = 200000 * 1024^2)
sessionInfo()
R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: AlmaLinux 9.3 (Shamrock Pampas Cat) Matrix products: default BLAS/LAPACK: /hpc/group/pbenfeylab/tmn23/miniconda3/envs/muscat/lib/libopenblasp-r0.3.21.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] future_1.31.0 scran_1.26.0 [3] scuttle_1.8.0 SingleCellExperiment_1.20.0 [5] SummarizedExperiment_1.28.0 Biobase_2.58.0 [7] GenomicRanges_1.50.0 GenomeInfoDb_1.34.8 [9] IRanges_2.32.0 S4Vectors_0.36.0 [11] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 [13] matrixStats_0.63.0 limma_3.54.0 [15] muscat_1.12.0 ggrepel_0.9.3 [17] gprofiler2_0.2.1 GeneOverlap_1.34.0 [19] circlize_0.4.15 ComplexHeatmap_2.14.0 [21] cowplot_1.1.1 SeuratObject_4.1.3 [23] Seurat_4.3.0 lubridate_1.9.2 [25] forcats_1.0.0 stringr_1.5.0 [27] dplyr_1.1.0 purrr_1.0.1 [29] readr_2.1.4 tidyr_1.3.0 [31] tibble_3.1.8 ggplot2_3.4.1 [33] tidyverse_2.0.0 loaded via a namespace (and not attached): [1] pbdZMQ_0.3-9 scattermore_0.8 [3] bit64_4.0.5 irlba_2.3.5.1 [5] DelayedArray_0.24.0 data.table_1.14.8 [7] KEGGREST_1.38.0 RCurl_1.98-1.10 [9] doParallel_1.0.17 generics_0.1.3 [11] ScaledMatrix_1.6.0 RhpcBLASctl_0.23-42 [13] RSQLite_2.2.20 RANN_2.6.1 [15] bit_4.0.5 tzdb_0.3.0 [17] spatstat.data_3.0-0 httpuv_1.6.9 [19] viridis_0.6.2 hms_1.1.2 [21] evaluate_0.20 promises_1.2.0.1 [23] fansi_1.0.4 progress_1.2.2 [25] caTools_1.18.2 igraph_1.3.5 [27] DBI_1.1.3 geneplotter_1.76.0 [29] htmlwidgets_1.6.1 spatstat.geom_3.0-6 [31] ellipsis_0.3.2 backports_1.4.1 [33] annotate_1.76.0 aod_1.3.2 [35] deldir_1.0-6 sparseMatrixStats_1.10.0 [37] vctrs_0.5.2 ROCR_1.0-11 [39] abind_1.4-5 cachem_1.0.6 [41] withr_2.5.0 progressr_0.13.0 [43] sctransform_0.3.5 prettyunits_1.1.1 [45] goftest_1.2-3 cluster_2.1.4 [47] IRdisplay_1.1 lazyeval_0.2.2 [49] crayon_1.5.2 genefilter_1.80.0 [51] spatstat.explore_3.0-6 edgeR_3.40.0 [53] pkgconfig_2.0.3 nlme_3.1-162 [55] vipor_0.4.5 blme_1.0-5 [57] rlang_1.0.6 globals_0.16.2 [59] lifecycle_1.0.3 miniUI_0.1.1.1 [61] rsvd_1.0.5 polyclip_1.10-4 [63] lmtest_0.9-40 Matrix_1.5-3 [65] IRkernel_1.3.2 boot_1.3-28.1 [67] zoo_1.8-11 base64enc_0.1-3 [69] beeswarm_0.4.0 ggridges_0.5.4 [71] GlobalOptions_0.1.2 png_0.1-8 [73] viridisLite_0.4.1 rjson_0.2.21 [75] bitops_1.0-7 KernSmooth_2.23-20 [77] Biostrings_2.66.0 blob_1.2.3 [79] DelayedMatrixStats_1.20.0 shape_1.4.6 [81] parallelly_1.34.0 spatstat.random_3.1-3 [83] beachmat_2.14.0 scales_1.2.1 [85] memoise_2.0.1 magrittr_2.0.3 [87] plyr_1.8.8 ica_1.0-3 [89] gplots_3.1.3 zlibbioc_1.44.0 [91] compiler_4.2.2 dqrng_0.3.0 [93] RColorBrewer_1.1-3 clue_0.3-64 [95] lme4_1.1-31 DESeq2_1.38.0 [97] fitdistrplus_1.1-8 cli_3.6.0 [99] XVector_0.38.0 lmerTest_3.1-3 [101] listenv_0.9.0 patchwork_1.1.2 [103] pbapply_1.7-0 TMB_1.9.2 [105] MASS_7.3-58.2 tidyselect_1.2.0 [107] stringi_1.7.12 BiocSingular_1.14.0 [109] locfit_1.5-9.7 tools_4.2.2 [111] timechange_0.2.0 future.apply_1.10.0 [113] parallel_4.2.2 uuid_1.1-0 [115] bluster_1.8.0 foreach_1.5.2 [117] metapod_1.6.0 gridExtra_2.3 [119] Rtsne_0.16 digest_0.6.31 [121] shiny_1.7.4 Rcpp_1.0.10 [123] broom_1.0.3 later_1.3.0 [125] RcppAnnoy_0.0.20 httr_1.4.4 [127] AnnotationDbi_1.60.0 Rdpack_2.4 [129] colorspace_2.1-0 XML_3.99-0.13 [131] tensor_1.5 reticulate_1.28 [133] splines_4.2.2 statmod_1.5.0 [135] uwot_0.1.14 spatstat.utils_3.0-1 [137] scater_1.26.0 sp_1.6-0 [139] plotly_4.10.1 xtable_1.8-4 [141] jsonlite_1.8.4 nloptr_2.0.3 [143] R6_2.5.1 pillar_1.8.1 [145] htmltools_0.5.4 mime_0.12 [147] glue_1.6.2 fastmap_1.1.0 [149] minqa_1.2.5 BiocParallel_1.32.5 [151] BiocNeighbors_1.16.0 codetools_0.2-19 [153] utf8_1.2.3 lattice_0.20-45 [155] spatstat.sparse_3.0-0 numDeriv_2016.8-1.1 [157] pbkrtest_0.5.2 ggbeeswarm_0.7.1 [159] leiden_0.4.3 gtools_3.9.4 [161] survival_3.5-3 glmmTMB_1.1.5 [163] repr_1.1.6 munsell_0.5.0 [165] GetoptLong_1.0.5 GenomeInfoDbData_1.2.9 [167] iterators_1.0.14 variancePartition_1.28.0 [169] reshape2_1.4.4 gtable_0.3.1 [171] rbibutils_2.2.13
rc.integrated <- readRDS("../../CheWei/scRNA-seq/Integrated_Objects/rc.integrated_8S_CVP_BRI1_seu3_annotated_20230316.rds")
rc.integrated
An object of class Seurat 71788 features across 55427 samples within 3 assays Active assay: SCT (25288 features, 0 variable features) 2 other assays present: RNA, integrated 4 dimensional reductions calculated: pca, umap, umap_3D, umap_2D
rc.integrated <- subset(rc.integrated,
subset = orig.ident %in% c("sc_130",
"sc_131",
"sc_132",
"sc_134",
"sc_135",
"sc_136"))
table(rc.integrated$orig.ident, rc.integrated$geno)
WT bri1_T pCVP2_BRI1_Citrine_bri1_T
sc_130 6589 0 0
sc_131 0 7615 0
sc_132 0 0 6550
sc_134 7745 0 0
sc_135 0 5038 0
sc_136 0 0 6089
feature_names <- read_tsv("../data/features.tsv.gz", col_names = c("AGI", "Name", "Type")) %>%
select(-Type) %>%
distinct()
Rows: 32833 Columns: 3 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "\t" chr (3): AGI, Name, Type ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
rc.integrated$geno <- factor(rc.integrated$geno, levels=c("WT", "bri1_T", "pCVP2_BRI1_Citrine_bri1_T"))
time_zonecell_typetime_zone_cell_typeorder <- c("Quiescent Center", "Ground Tissue","Columella", "Lateral Root Cap", "Atrichoblast", "Trichoblast", "Cortex", "Endodermis", "Phloem","Protophloem", "Xylem", "Procambium","Pericycle","Phloem Pole Pericycle", "Protoxylem", "Metaxylem", "Unknown")
palette <- c("#9400D3", "#DCD0FF","#5AB953", "#BFEF45", "#008080", "#21B6A8", "#82B6FF", "#0000FF","#E6194B", "#DD77EC", "#9A6324", "#FFE119", "#FF9900", "#FFD4E3", "#9A6324", "#DDAA6F", "#EEEEEE")
rc.integrated$cell_type <- factor(rc.integrated$cell_type, levels = order[sort(match(unique(rc.integrated$cell_type),order))])
color <- palette[sort(match(unique(rc.integrated$cell_type),order))]
options(repr.plot.width=16.5, repr.plot.height=6)
(Celltype_umap <- DimPlot(rc.integrated,
reduction = "umap",
group.by = "cell_type",
cols = color, split.by = 'geno',
ncol=3,
pt.size = 0.5))
ggsave("../output/CVP/Cell_type_umap_square_all_samples.pdf", width=16.5, height=6)
options(repr.plot.width = 18, repr.plot.height = 6)
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="BRI1-mCitrine", split.by = "geno", order=T, max.cutoff = "q90", pt.size = 0.5)
ggsave("../output/CVP/BRI1-mCitrine_expression_all_samples.pdf", width=18.3, height=6)
Warning message in FeaturePlot(rc.integrated, features = "BRI1-mCitrine", split.by = "geno", : “All cells have the same value (0) of BRI1-mCitrine.”
# expression of CVP2
options(repr.plot.width = 18, repr.plot.height = 6)
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="AT1G05470", split.by = "geno", order=T, max.cutoff = "q90", pt.size = 0.5)
ggsave("../output/CVP/CVP2_AT1G05470_expression_all_samples.pdf", width=18.3, height=6)
options(repr.plot.width=30, repr.plot.height=7)
DimPlot(rc.integrated, reduction = "umap", group.by = "cell_type", cols = color, split.by = 'orig.ident', pt.size = 0.75, ncol=8)
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="BRI1-mCitrine", split.by = "orig.ident", order=T, max.cutoff = "q80", pt.size = 0.5)
Warning message in FeaturePlot(rc.integrated, features = "BRI1-mCitrine", split.by = "orig.ident", : “All cells have the same value (0) of BRI1-mCitrine.” Warning message in FeaturePlot(rc.integrated, features = "BRI1-mCitrine", split.by = "orig.ident", : “All cells have the same value (0) of BRI1-mCitrine.”
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="AT1G05470", split.by = "orig.ident", order=T, max.cutoff = "q80", pt.size = 0.5)
table(rc.integrated$orig.ident, rc.integrated$cell_type)
Columella Lateral Root Cap Atrichoblast Trichoblast Cortex Endodermis
sc_130 895 1058 1445 1000 972 725
sc_131 672 1800 1441 900 777 490
sc_132 474 1597 1089 916 720 544
sc_134 582 2101 1171 1041 906 573
sc_135 294 991 1055 707 544 480
sc_136 649 1240 1176 871 878 617
Phloem Xylem Procambium Pericycle
sc_130 52 172 127 143
sc_131 130 273 320 812
sc_132 138 230 288 554
sc_134 123 267 348 633
sc_135 88 191 260 428
sc_136 78 147 186 247
table(rc.integrated$orig.ident, rc.integrated$time_zone)
Distal Columella Distal Lateral Root Cap Elongation Maturation
sc_130 834 699 2433 1206
sc_131 626 566 1873 1430
sc_132 442 678 1950 1511
sc_134 535 971 2472 1673
sc_135 268 201 1110 930
sc_136 610 581 2009 1302
Meristem Proximal Columella Proximal Lateral Root Cap
sc_130 998 60 359
sc_131 1887 36 1197
sc_132 1023 31 915
sc_134 921 44 1129
sc_135 1730 26 773
sc_136 891 37 659
# construct sce manually
my_metadata <- data.frame(sample_id = rc.integrated$orig.ident,
group_id = rc.integrated$geno,
cluster_id = rc.integrated$cell_type,
date=rc.integrated$rep) # include experimental rep as co-variate
sce <- SingleCellExperiment(assays = list(counts = rc.integrated@assays$RNA@counts),
colData = my_metadata)
(sce <- prepSCE(sce,
kid = "cluster_id", # subpopulation assignments
gid = "group_id", # group IDs (ctrl/stim)
sid = "sample_id", # sample IDs (ctrl/stim.1234)
drop = FALSE)) # drop all other colData columns
class: SingleCellExperiment dim: 28980 39626 metadata(1): experiment_info assays(1): counts rownames(28980): AT1G01010 AT1G01020 ... AT5G39430 AT5G54075 rowData names(0): colnames(39626): AAACCCACAACAGCCC_6 AAACCCACAGAGTAAT_6 ... TTTGTTGCATCGATAC_11 TTTGTTGTCAAGAGGC_11 colData names(4): cluster_id sample_id group_id date reducedDimNames(0): mainExpName: NULL altExpNames(0):
# remove undetected genes
sce <- sce[rowSums(counts(sce) > 0) > 0, ]
dim(sce)
# create pseudobulk profiles
pb <- aggregateData(sce,
assay = "counts", fun = "sum",
by = c("cluster_id", "sample_id"))
# one sheet per subpopulation
assayNames(pb)
# pseudobulks for 1st subpopulation
t(head(assay(pb)))
| AT1G01010 | AT1G01020 | AT1G03987 | AT1G01030 | AT1G01040 | AT1G01050 | |
|---|---|---|---|---|---|---|
| sc_130 | 68 | 97 | 1 | 21 | 19 | 1846 |
| sc_131 | 46 | 92 | 0 | 10 | 17 | 1092 |
| sc_132 | 32 | 52 | 0 | 10 | 10 | 901 |
| sc_134 | 46 | 73 | 0 | 18 | 14 | 1210 |
| sc_135 | 14 | 57 | 0 | 11 | 10 | 623 |
| sc_136 | 55 | 81 | 0 | 19 | 16 | 1440 |
# experiment info for contrasts, add dates from csv
ei <- metadata(sce)$experiment_info
ei
ei$rep <- c(1, 1, 1, 2, 2, 2)
ei
#sample_date <- select(bscs, sample_id=sample, date=rep)
#ei <- left_join(ei, sample_date)
#ei
| sample_id | group_id | n_cells |
|---|---|---|
| <fct> | <fct> | <dbl> |
| sc_130 | WT | 6589 |
| sc_131 | bri1_T | 7615 |
| sc_132 | pCVP2_BRI1_Citrine_bri1_T | 6550 |
| sc_134 | WT | 7745 |
| sc_135 | bri1_T | 5038 |
| sc_136 | pCVP2_BRI1_Citrine_bri1_T | 6089 |
| sample_id | group_id | n_cells | rep |
|---|---|---|---|
| <fct> | <fct> | <dbl> | <dbl> |
| sc_130 | WT | 6589 | 1 |
| sc_131 | bri1_T | 7615 | 1 |
| sc_132 | pCVP2_BRI1_Citrine_bri1_T | 6550 | 1 |
| sc_134 | WT | 7745 | 2 |
| sc_135 | bri1_T | 5038 | 2 |
| sc_136 | pCVP2_BRI1_Citrine_bri1_T | 6089 | 2 |
mm <- model.matrix(~ 0 + ei$group_id + ei$rep)
dimnames(mm) <- list(ei$sample_id, c(levels(ei$group_id), "rep"))
mm
| WT | bri1_T | pCVP2_BRI1_Citrine_bri1_T | rep | |
|---|---|---|---|---|
| sc_130 | 1 | 0 | 0 | 1 |
| sc_131 | 0 | 1 | 0 | 1 |
| sc_132 | 0 | 0 | 1 | 1 |
| sc_134 | 1 | 0 | 0 | 2 |
| sc_135 | 0 | 1 | 0 | 2 |
| sc_136 | 0 | 0 | 1 | 2 |
contrast <- makeContrasts("pCVP2_BRI1_Citrine_bri1_T-bri1_T",
"pCVP2_BRI1_Citrine_bri1_T-WT", levels = mm)
contrast
| pCVP2_BRI1_Citrine_bri1_T-bri1_T | pCVP2_BRI1_Citrine_bri1_T-WT | |
|---|---|---|
| WT | 0 | -1 |
| bri1_T | -1 | 0 |
| pCVP2_BRI1_Citrine_bri1_T | 1 | 1 |
| rep | 0 | 0 |
res <- pbDS(pb, design = mm,
contrast = contrast,
method="edgeR",
min_cells=5,
filter = c("none"))
|======================================================================| 100%
# DEG results with gene freqs
(res_to_write_frq <- resDS(sce, res, bind = "row", cpm=TRUE, frq=T))
| gene | cluster_id | sc_130.cpm | sc_134.cpm | sc_131.cpm | sc_135.cpm | sc_132.cpm | sc_136.cpm | sc_130.frq | sc_134.frq | ⋯ | WT.frq | bri1_T.frq | pCVP2_BRI1_Citrine_bri1_T.frq | logFC | logCPM | F | p_val | p_adj.loc | p_adj.glb | contrast |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | ⋯ | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> |
| AT1G01010 | Columella | 9.860 | 9.66 | 8.300 | 4.610 | 9.790 | 10.200 | 0.07260 | 0.06870 | ⋯ | 0.071100 | 0.06110 | 0.07480 | 0.606000 | 3.2200 | 4.05e+00 | 0.04420 | 0.3010 | 0.2410 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01010 | Columella | 9.860 | 9.66 | 8.300 | 4.610 | 9.790 | 10.200 | 0.07260 | 0.06870 | ⋯ | 0.071100 | 0.06110 | 0.07480 | 0.057900 | 3.2200 | 4.42e-02 | 0.83300 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01020 | Columella | 14.100 | 15.30 | 16.600 | 18.800 | 15.900 | 15.000 | 0.09610 | 0.10300 | ⋯ | 0.098800 | 0.13700 | 0.09880 | -0.193000 | 4.0200 | 6.53e-01 | 0.41900 | 0.8640 | 0.7690 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01020 | Columella | 14.100 | 15.30 | 16.600 | 18.800 | 15.900 | 15.000 | 0.09610 | 0.10300 | ⋯ | 0.098800 | 0.13700 | 0.09880 | 0.068000 | 4.0200 | 8.37e-02 | 0.77200 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G03987 | Columella | 0.145 | 0.00 | 0.000 | 0.000 | 0.000 | 0.000 | 0.00112 | 0.00000 | ⋯ | 0.000677 | 0.00000 | 0.00000 | 0.394000 | -1.1500 | 2.05e-09 | 1.00000 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G03987 | Columella | 0.145 | 0.00 | 0.000 | 0.000 | 0.000 | 0.000 | 0.00112 | 0.00000 | ⋯ | 0.000677 | 0.00000 | 0.00000 | -1.760000 | -1.1500 | 2.16e-01 | 0.64200 | 1.0000 | 0.9950 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01030 | Columella | 3.050 | 3.78 | 1.800 | 3.620 | 3.060 | 3.520 | 0.02230 | 0.02750 | ⋯ | 0.024400 | 0.01970 | 0.02320 | 0.331000 | 1.8100 | 4.76e-01 | 0.49000 | 0.8760 | 0.7970 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01030 | Columella | 3.050 | 3.78 | 1.800 | 3.620 | 3.060 | 3.520 | 0.02230 | 0.02750 | ⋯ | 0.024400 | 0.01970 | 0.02320 | -0.076900 | 1.8100 | 3.08e-02 | 0.86100 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01040 | Columella | 2.760 | 2.94 | 3.070 | 3.290 | 3.060 | 2.970 | 0.02010 | 0.02410 | ⋯ | 0.021700 | 0.02590 | 0.01960 | -0.078900 | 1.7700 | 2.77e-02 | 0.86800 | 1.0000 | 0.9800 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01040 | Columella | 2.760 | 2.94 | 3.070 | 3.290 | 3.060 | 2.970 | 0.02010 | 0.02410 | ⋯ | 0.021700 | 0.02590 | 0.01960 | 0.076100 | 1.7700 | 2.75e-02 | 0.86800 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01050 | Columella | 268.000 | 254.00 | 197.000 | 205.000 | 276.000 | 267.000 | 0.76800 | 0.72700 | ⋯ | 0.752000 | 0.73500 | 0.76800 | 0.433000 | 7.9400 | 9.27e+00 | 0.00233 | 0.0367 | 0.0362 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01050 | Columella | 268.000 | 254.00 | 197.000 | 205.000 | 276.000 | 267.000 | 0.76800 | 0.72700 | ⋯ | 0.752000 | 0.73500 | 0.76800 | 0.056500 | 7.9400 | 1.61e-01 | 0.68800 | 1.0000 | 0.9980 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01060 | Columella | 0.435 | 0.84 | 0.722 | 0.988 | 0.306 | 0.556 | 0.00335 | 0.00687 | ⋯ | 0.004740 | 0.00725 | 0.00356 | -0.975000 | 0.0563 | 5.80e-01 | 0.44600 | 0.8640 | 0.7870 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01060 | Columella | 0.435 | 0.84 | 0.722 | 0.988 | 0.306 | 0.556 | 0.00335 | 0.00687 | ⋯ | 0.004740 | 0.00725 | 0.00356 | -0.510000 | 0.0563 | 1.60e-01 | 0.68900 | 1.0000 | 0.9980 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01070 | Columella | 0.145 | 0.21 | 1.440 | 0.329 | 0.612 | 0.185 | 0.00112 | 0.00172 | ⋯ | 0.001350 | 0.00932 | 0.00178 | -1.160000 | -0.1510 | 6.59e-01 | 0.41700 | 0.8640 | 0.7680 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01070 | Columella | 0.145 | 0.21 | 1.440 | 0.329 | 0.612 | 0.185 | 0.00112 | 0.00172 | ⋯ | 0.001350 | 0.00932 | 0.00178 | 1.120000 | -0.1510 | 4.07e-01 | 0.52400 | 1.0000 | 0.9810 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01080 | Columella | 0.435 | 0.42 | 0.722 | 0.658 | 0.306 | 0.371 | 0.00335 | 0.00344 | ⋯ | 0.003390 | 0.00621 | 0.00267 | -0.960000 | -0.1520 | 4.20e-01 | 0.51700 | 0.8820 | 0.8020 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01080 | Columella | 0.435 | 0.42 | 0.722 | 0.658 | 0.306 | 0.371 | 0.00335 | 0.00344 | ⋯ | 0.003390 | 0.00621 | 0.00267 | -0.291000 | -0.1520 | 3.71e-02 | 0.84700 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01090 | Columella | 38.000 | 39.10 | 41.700 | 41.500 | 38.300 | 38.800 | 0.24200 | 0.25900 | ⋯ | 0.249000 | 0.28900 | 0.25600 | -0.111000 | 5.3200 | 3.70e-01 | 0.54300 | 0.8920 | 0.8080 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01090 | Columella | 38.000 | 39.10 | 41.700 | 41.500 | 38.300 | 38.800 | 0.24200 | 0.25900 | ⋯ | 0.249000 | 0.28900 | 0.25600 | -0.000277 | 5.3200 | 2.37e-06 | 0.99900 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01100 | Columella | 267.000 | 297.00 | 407.000 | 492.000 | 325.000 | 343.000 | 0.74600 | 0.76500 | ⋯ | 0.754000 | 0.89500 | 0.81700 | -0.423000 | 8.4700 | 9.84e+00 | 0.00171 | 0.0290 | 0.0293 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01100 | Columella | 267.000 | 297.00 | 407.000 | 492.000 | 325.000 | 343.000 | 0.74600 | 0.76500 | ⋯ | 0.754000 | 0.89500 | 0.81700 | 0.246000 | 8.4700 | 3.33e+00 | 0.06820 | 1.0000 | 0.8040 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01110 | Columella | 2.180 | 2.52 | 2.160 | 0.658 | 3.060 | 1.670 | 0.01680 | 0.01890 | ⋯ | 0.017600 | 0.01350 | 0.01600 | 0.623000 | 1.3100 | 1.05e+00 | 0.30500 | 0.7890 | 0.6810 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01110 | Columella | 2.180 | 2.52 | 2.160 | 0.658 | 3.060 | 1.670 | 0.01680 | 0.01890 | ⋯ | 0.017600 | 0.01350 | 0.01600 | -0.015900 | 1.3100 | 8.72e-04 | 0.97600 | 1.0000 | 1.0000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01120 | Columella | 2.030 | 3.15 | 1.980 | 0.658 | 3.670 | 2.970 | 0.01450 | 0.02410 | ⋯ | 0.018300 | 0.01240 | 0.01870 | 1.170000 | 1.5100 | 4.42e+00 | 0.03560 | 0.2620 | 0.2120 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01120 | Columella | 2.030 | 3.15 | 1.980 | 0.658 | 3.670 | 2.970 | 0.01450 | 0.02410 | ⋯ | 0.018300 | 0.01240 | 0.01870 | 0.373000 | 1.5100 | 5.95e-01 | 0.44000 | 1.0000 | 0.9810 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01130 | Columella | 0.435 | 1.26 | 1.080 | 0.658 | 1.840 | 0.927 | 0.00335 | 0.01030 | ⋯ | 0.006090 | 0.00828 | 0.00980 | 0.508000 | 0.4770 | 3.13e-01 | 0.57600 | 0.8920 | 0.8250 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01130 | Columella | 0.435 | 1.26 | 1.080 | 0.658 | 1.840 | 0.927 | 0.00335 | 0.01030 | ⋯ | 0.006090 | 0.00828 | 0.00980 | 0.702000 | 0.4770 | 6.49e-01 | 0.42000 | 1.0000 | 0.9810 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G01140 | Columella | 24.200 | 16.20 | 14.100 | 9.220 | 12.900 | 18.900 | 0.16000 | 0.11700 | ⋯ | 0.143000 | 0.10000 | 0.12000 | 0.482000 | 4.0700 | 3.76e+00 | 0.05240 | 0.3320 | 0.2670 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G01140 | Columella | 24.200 | 16.20 | 14.100 | 9.220 | 12.900 | 18.900 | 0.16000 | 0.11700 | ⋯ | 0.143000 | 0.10000 | 0.12000 | -0.290000 | 4.0700 | 1.62e+00 | 0.20200 | 1.0000 | 0.9810 | pCVP2_BRI1_Citrine_bri1_T-WT |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋱ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AT1G49205 | Pericycle | 0 | 0.2940 | 0 | 0.0000 | 0 | 0.5790 | 0 | 0.00790 | ⋯ | 0.00644 | 0.000000 | 0.00749 | 4.6900 | -1.72 | 4.54e+00 | 0.0748 | 0.497 | 0.329 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G49205 | Pericycle | 0 | 0.2940 | 0 | 0.0000 | 0 | 0.5790 | 0 | 0.00790 | ⋯ | 0.00644 | 0.000000 | 0.00749 | 0.8970 | -1.72 | 4.59e-01 | 0.5220 | 0.901 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT2G07975 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | 0.0461 | -2.55 | 3.22e-11 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT2G07975 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | -2.1600 | -2.55 | 4.11e-01 | 0.5440 | 0.901 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT3G53070 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | 0.0461 | -2.55 | 3.22e-11 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT3G53070 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | -2.1600 | -2.55 | 4.11e-01 | 0.5440 | 0.901 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT3G08325 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | 0.0461 | -2.55 | 3.22e-11 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT3G08325 | Pericycle | 0 | 0.0588 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00158 | ⋯ | 0.00129 | 0.000000 | 0.00000 | -2.1600 | -2.55 | 4.11e-01 | 0.5440 | 0.901 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT5G17345 | Pericycle | 0 | 0.1180 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00316 | ⋯ | 0.00258 | 0.000000 | 0.00000 | 0.0682 | -2.45 | 3.54e-11 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT5G17345 | Pericycle | 0 | 0.1180 | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.00316 | ⋯ | 0.00258 | 0.000000 | 0.00000 | -2.8700 | -2.45 | 8.24e-01 | 0.3970 | 0.852 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G43722 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G43722 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT1G60025 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT1G60025 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT3G04440 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT3G04440 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT3G25014 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT3G25014 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT4G03765 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT4G03765 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT4G10190 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | -2.0700 | -2.55 | 5.18e-01 | 0.4970 | 0.811 | 0.799 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT4G10190 | Pericycle | 0 | 0.0000 | 0 | 0.0797 | 0 | 0.0000 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000806 | 0.00000 | 0.6950 | -2.55 | 2.79e-09 | 1.0000 | 1.000 | 1.000 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT2G19010 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.0965 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 2.3500 | -2.55 | 6.80e-01 | 0.4400 | 0.811 | 0.783 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT2G19010 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.0965 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 2.9800 | -2.55 | 8.31e-01 | 0.3950 | 0.852 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT2G05645 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.1930 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 3.2100 | -2.44 | 1.36e+00 | 0.2860 | 0.756 | 0.662 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT2G05645 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.1930 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 3.9500 | -2.44 | 1.65e+00 | 0.2440 | 0.806 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT3G20362 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.7720 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00999 | 5.0900 | -1.91 | 5.34e+00 | 0.0579 | 0.455 | 0.284 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT3G20362 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.7720 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00999 | 5.9400 | -1.91 | 6.41e+00 | 0.0424 | 0.592 | 0.707 | pCVP2_BRI1_Citrine_bri1_T-WT |
| AT4G03040 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.0965 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 2.3500 | -2.55 | 6.80e-01 | 0.4400 | 0.811 | 0.783 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| AT4G03040 | Pericycle | 0 | 0.0000 | 0 | 0.0000 | 0 | 0.0965 | 0 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.00125 | 2.9800 | -2.55 | 8.31e-01 | 0.3950 | 0.852 | 0.981 | pCVP2_BRI1_Citrine_bri1_T-WT |
## all genes as background
all_bg <- res_to_write_frq
all_bg %>% filter(gene=="BRI1-mCitrine") %>%
arrange(desc(sc_136.cpm))
| gene | cluster_id | sc_130.cpm | sc_134.cpm | sc_131.cpm | sc_135.cpm | sc_132.cpm | sc_136.cpm | sc_130.frq | sc_134.frq | ⋯ | WT.frq | bri1_T.frq | pCVP2_BRI1_Citrine_bri1_T.frq | logFC | logCPM | F | p_val | p_adj.loc | p_adj.glb | contrast |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | ⋯ | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <chr> |
| BRI1-mCitrine | Atrichoblast | 0 | 0 | 0.1760 | 0.0766 | 5.090 | 8.22 | 0 | 0 | ⋯ | 0 | 0.00280 | 0.0870 | 5.60 | 1.1000 | 133.00 | 1.68e-07 | 2.16e-05 | 5.72e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Atrichoblast | 0 | 0 | 0.1760 | 0.0766 | 5.090 | 8.22 | 0 | 0 | ⋯ | 0 | 0.00280 | 0.0870 | 10.20 | 1.1000 | 160.00 | 6.42e-08 | 7.86e-04 | 1.30e-04 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Columella | 0 | 0 | 0.3610 | 0.3290 | 5.810 | 7.60 | 0 | 0 | ⋯ | 0 | 0.00311 | 0.0490 | 4.12 | 1.4000 | 37.30 | 1.01e-09 | 1.34e-07 | 1.02e-06 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Columella | 0 | 0 | 0.3610 | 0.3290 | 5.810 | 7.60 | 0 | 0 | ⋯ | 0 | 0.00311 | 0.0490 | 7.99 | 1.4000 | 66.20 | 4.22e-16 | 1.09e-12 | 8.64e-12 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Lateral Root Cap | 0 | 0 | 0.0515 | 0.1630 | 3.080 | 3.94 | 0 | 0 | ⋯ | 0 | 0.00107 | 0.0271 | 5.03 | 0.3110 | 60.80 | 4.33e-05 | 3.70e-03 | 2.26e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Lateral Root Cap | 0 | 0 | 0.0515 | 0.1630 | 3.080 | 3.94 | 0 | 0 | ⋯ | 0 | 0.00107 | 0.0271 | 8.67 | 0.3110 | 72.80 | 2.22e-05 | 1.37e-01 | 1.29e-02 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Trichoblast | 0 | 0 | 0.4060 | 0.3200 | 3.200 | 2.59 | 0 | 0 | ⋯ | 0 | 0.00871 | 0.0862 | 2.98 | 0.2080 | 50.70 | 2.01e-05 | 2.52e-03 | 1.29e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Trichoblast | 0 | 0 | 0.4060 | 0.3200 | 3.200 | 2.59 | 0 | 0 | ⋯ | 0 | 0.00871 | 0.0862 | 9.36 | 0.2080 | 157.00 | 7.98e-08 | 6.49e-04 | 1.56e-04 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Phloem | 0 | 0 | 0.0000 | 0.0000 | 0.000 | 2.56 | 0 | 0 | ⋯ | 0 | 0.00000 | 0.0139 | 4.12 | 0.6840 | 1.54 | 2.15e-01 | 9.13e-01 | 5.81e-01 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Phloem | 0 | 0 | 0.0000 | 0.0000 | 0.000 | 2.56 | 0 | 0 | ⋯ | 0 | 0.00000 | 0.0139 | 4.61 | 0.6840 | 1.88 | 1.71e-01 | 1.00e+00 | 9.61e-01 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Xylem | 0 | 0 | 0.3750 | 0.2570 | 0.794 | 2.18 | 0 | 0 | ⋯ | 0 | 0.00647 | 0.0345 | 1.99 | -0.0746 | 2.98 | 1.03e-01 | 4.84e-01 | 3.95e-01 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Xylem | 0 | 0 | 0.3750 | 0.2570 | 0.794 | 2.18 | 0 | 0 | ⋯ | 0 | 0.00647 | 0.0345 | 5.95 | -0.0746 | 11.40 | 3.87e-03 | 2.38e-01 | 2.71e-01 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Procambium | 0 | 0 | 0.0000 | 0.0000 | 2.790 | 2.12 | 0 | 0 | ⋯ | 0 | 0.00000 | 0.0443 | 6.67 | 0.3190 | 19.70 | 1.92e-04 | 1.05e-02 | 6.44e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Procambium | 0 | 0 | 0.0000 | 0.0000 | 2.790 | 2.12 | 0 | 0 | ⋯ | 0 | 0.00000 | 0.0443 | 6.57 | 0.3190 | 16.00 | 5.76e-04 | 8.88e-02 | 9.90e-02 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Pericycle | 0 | 0 | 0.4970 | 0.4780 | 2.660 | 2.03 | 0 | 0 | ⋯ | 0 | 0.01130 | 0.0724 | 2.25 | 0.2310 | 19.50 | 2.78e-03 | 1.41e-01 | 4.09e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Pericycle | 0 | 0 | 0.4970 | 0.4780 | 2.660 | 2.03 | 0 | 0 | ⋯ | 0 | 0.01130 | 0.0724 | 7.82 | 0.2310 | 48.40 | 1.76e-04 | 2.48e-01 | 5.04e-02 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Cortex | 0 | 0 | 0.2090 | 0.1940 | 1.420 | 1.68 | 0 | 0 | ⋯ | 0 | 0.00454 | 0.0300 | 2.89 | -0.4290 | 18.50 | 2.56e-03 | 5.77e-02 | 3.87e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Cortex | 0 | 0 | 0.2090 | 0.1940 | 1.420 | 1.68 | 0 | 0 | ⋯ | 0 | 0.00454 | 0.0300 | 7.55 | -0.4290 | 41.30 | 1.98e-04 | 1.99e-01 | 5.42e-02 | pCVP2_BRI1_Citrine_bri1_T-WT |
| BRI1-mCitrine | Endodermis | 0 | 0 | 0.3760 | 0.3890 | 0.508 | 1.36 | 0 | 0 | ⋯ | 0 | 0.00825 | 0.0233 | 1.22 | -0.7470 | 2.41 | 1.60e-01 | 5.36e-01 | 5.00e-01 | pCVP2_BRI1_Citrine_bri1_T-bri1_T |
| BRI1-mCitrine | Endodermis | 0 | 0 | 0.3760 | 0.3890 | 0.508 | 1.36 | 0 | 0 | ⋯ | 0 | 0.00825 | 0.0233 | 6.60 | -0.7470 | 22.00 | 1.62e-03 | 4.73e-01 | 1.78e-01 | pCVP2_BRI1_Citrine_bri1_T-WT |
length(unique(all_bg$gene))
#total DE genes p_adj.loc < 0.05, abs(logFC) > 1.5
sig_DE <- filter(res_to_write_frq, p_adj.loc<=0.05 & abs(logFC) > log2(1.5))
sig_DE <- left_join(sig_DE, feature_names, by=c("gene"="AGI"))
length(unique(sig_DE$gene))
# filter gene freqs to avoid calling lowly detected genes
sig_DE_fil <- filter(sig_DE, WT.frq >=0.05 | bri1_T.frq >=0.05 | pCVP2_BRI1_Citrine_bri1_T.frq >=0.05)
length(unique(sig_DE_fil$gene))
# load TFs
TF_list <- read_csv("../data/Kay_TF_thalemine_annotations.csv", col_names = c("gene", "TF_Name", "Description"))
Rows: 2485 Columns: 3 ── Column specification ──────────────────────────────────────────────────────── Delimiter: "," chr (3): gene, TF_Name, Description ℹ Use `spec()` to retrieve the full column specification for this data. ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
sig_DE_fil <- left_join(sig_DE_fil, TF_list)
Joining with `by = join_by(gene)`
# label up vs down
sig_DE_fil <- sig_DE_fil %>%
mutate(up_dn_label = case_when(logFC >=log2(1.5) ~ "Up",
logFC <=log2(1/1.5) ~ "Down",
TRUE ~ "Not DE"))
sig_DE_fil$clust_up_dn <- paste(sig_DE_fil$cluster_id, sig_DE_fil$up_dn_label, sep="_")
sig_DE_fil
| gene | cluster_id | sc_130.cpm | sc_134.cpm | sc_131.cpm | sc_135.cpm | sc_132.cpm | sc_136.cpm | sc_130.frq | sc_134.frq | ⋯ | F | p_val | p_adj.loc | p_adj.glb | contrast | Name | TF_Name | Description | up_dn_label | clust_up_dn |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | ⋯ | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> |
| AT1G01240 | Columella | 31.90 | 25.20 | 15.30 | 14.20 | 23.00 | 30.00 | 0.2090 | 0.1800 | ⋯ | 15.40 | 8.59e-05 | 2.69e-03 | 3.66e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01240 | NA | NA | Up | Columella_Up |
| AT1G01580 | Columella | 41.20 | 32.80 | 15.20 | 18.10 | 35.50 | 32.60 | 0.2500 | 0.2160 | ⋯ | 26.50 | 2.70e-07 | 2.02e-05 | 7.79e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | FRO2 | NA | NA | Up | Columella_Up |
| AT1G01620 | Columella | 623.00 | 348.00 | 256.00 | 189.00 | 287.00 | 386.00 | 0.9340 | 0.8040 | ⋯ | 21.40 | 3.71e-06 | 1.97e-04 | 4.11e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | PIP1-3 | NA | NA | Up | Columella_Up |
| AT1G01640 | Columella | 10.70 | 10.50 | 3.07 | 6.58 | 12.20 | 7.97 | 0.0626 | 0.0687 | ⋯ | 12.30 | 4.50e-04 | 1.02e-02 | 1.17e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01640 | AT1G01640 | BTB/POZ domain-containing protein | Up | Columella_Up |
| AT1G01725 | Columella | 14.90 | 16.20 | 4.87 | 4.28 | 16.20 | 18.70 | 0.1030 | 0.1190 | ⋯ | 43.00 | 5.57e-11 | 9.57e-09 | 7.61e-08 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01725 | NA | NA | Up | Columella_Up |
| AT1G02430 | Columella | 8.99 | 7.98 | 5.23 | 3.29 | 6.73 | 11.70 | 0.0648 | 0.0619 | ⋯ | 10.70 | 1.10e-03 | 2.06e-02 | 2.17e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ATARFD1B | NA | NA | Up | Columella_Up |
| AT1G02610 | Columella | 23.10 | 23.30 | 13.50 | 10.90 | 23.60 | 22.60 | 0.1450 | 0.1580 | ⋯ | 15.30 | 9.08e-05 | 2.81e-03 | 3.80e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G02610 | NA | NA | Up | Columella_Up |
| AT1G02860 | Columella | 70.90 | 71.80 | 51.40 | 38.50 | 77.40 | 70.30 | 0.3270 | 0.3280 | ⋯ | 16.50 | 4.82e-05 | 1.66e-03 | 2.43e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | BAH1 | NA | NA | Up | Columella_Up |
| AT1G02870 | Columella | 6.24 | 17.00 | 18.60 | 22.70 | 11.90 | 11.70 | 0.0425 | 0.0945 | ⋯ | 11.60 | 6.48e-04 | 1.36e-02 | 1.51e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G02870 | NA | NA | Down | Columella_Down |
| AT1G03030 | Columella | 19.70 | 19.70 | 13.20 | 14.80 | 19.90 | 24.90 | 0.1400 | 0.1370 | ⋯ | 8.76 | 3.07e-03 | 4.53e-02 | 4.38e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03030 | NA | NA | Up | Columella_Up |
| AT1G03200 | Columella | 14.20 | 13.40 | 4.69 | 6.91 | 12.90 | 13.50 | 0.0883 | 0.1030 | ⋯ | 17.30 | 3.15e-05 | 1.17e-03 | 1.79e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03200 | NA | NA | Up | Columella_Up |
| AT1G03850 | Columella | 58.40 | 53.40 | 42.00 | 38.50 | 62.10 | 88.80 | 0.2980 | 0.2770 | ⋯ | 25.60 | 4.23e-07 | 2.97e-05 | 1.05e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03850 | NA | NA | Up | Columella_Up |
| AT1G03870 | Columella | 221.00 | 105.00 | 95.20 | 53.00 | 117.00 | 139.00 | 0.6830 | 0.4900 | ⋯ | 29.50 | 5.65e-08 | 4.88e-06 | 2.58e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | FLA9 | NA | NA | Up | Columella_Up |
| AT1G04100 | Columella | 22.20 | 24.40 | 36.10 | 35.60 | 24.50 | 21.10 | 0.1490 | 0.1600 | ⋯ | 11.00 | 9.21e-04 | 1.80e-02 | 1.93e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | IAA10 | IAA10 | indoleacetic acid-induced protein 10 | Down | Columella_Down |
| AT1G04180 | Columella | 20.30 | 20.20 | 6.13 | 9.22 | 11.00 | 10.00 | 0.0782 | 0.0893 | ⋯ | 15.10 | 1.03e-04 | 1.43e-02 | 3.56e-02 | pCVP2_BRI1_Citrine_bri1_T-WT | YUC9 | NA | NA | Down | Columella_Down |
| AT1G04280 | Columella | 14.10 | 13.40 | 5.23 | 4.61 | 14.40 | 13.40 | 0.0883 | 0.1010 | ⋯ | 24.70 | 6.79e-07 | 4.48e-05 | 1.45e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G04280 | NA | NA | Up | Columella_Up |
| AT1G04870 | Columella | 2.18 | 2.94 | 8.30 | 12.20 | 3.37 | 4.08 | 0.0168 | 0.0223 | ⋯ | 16.70 | 4.28e-05 | 1.51e-03 | 2.24e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | PRMT10 | NA | NA | Down | Columella_Down |
| AT1G05680 | Columella | 1080.00 | 1030.00 | 730.00 | 738.00 | 1180.00 | 1110.00 | 0.7550 | 0.6740 | ⋯ | 29.30 | 6.39e-08 | 5.49e-06 | 2.82e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | UGT74E2 | NA | NA | Up | Columella_Up |
| AT1G05840 | Columella | 7.54 | 9.24 | 3.25 | 5.93 | 10.40 | 7.23 | 0.0547 | 0.0739 | ⋯ | 8.60 | 3.36e-03 | 4.86e-02 | 4.65e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G05840 | NA | NA | Up | Columella_Up |
| AT1G06090 | Columella | 81.10 | 124.00 | 88.70 | 37.50 | 144.00 | 79.90 | 0.2020 | 0.2290 | ⋯ | 24.50 | 7.40e-07 | 4.81e-05 | 1.52e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G06090 | NA | NA | Up | Columella_Up |
| AT1G06330 | Columella | 54.40 | 46.40 | 20.20 | 21.10 | 34.30 | 41.70 | 0.2800 | 0.2440 | ⋯ | 20.80 | 5.25e-06 | 2.64e-04 | 5.20e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G06330 | NA | NA | Up | Columella_Up |
| AT1G07030 | Columella | 71.80 | 58.00 | 44.70 | 43.80 | 65.80 | 66.80 | 0.4010 | 0.3570 | ⋯ | 11.20 | 8.39e-04 | 1.67e-02 | 1.81e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07030 | NA | NA | Up | Columella_Up |
| AT1G07070 | Columella | 5.22 | 9.03 | 17.00 | 21.70 | 10.70 | 11.70 | 0.0402 | 0.0704 | ⋯ | 9.73 | 1.81e-03 | 3.02e-02 | 3.06e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RPL35AA | NA | NA | Down | Columella_Down |
| AT1G07160 | Columella | 209.00 | 149.00 | 113.00 | 116.00 | 179.00 | 253.00 | 0.5520 | 0.4600 | ⋯ | 36.70 | 1.38e-09 | 1.76e-07 | 1.31e-06 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07160 | NA | NA | Up | Columella_Up |
| AT1G07175 | Columella | 158.00 | 134.00 | 81.30 | 100.00 | 141.00 | 162.00 | 0.4590 | 0.4020 | ⋯ | 22.40 | 2.21e-06 | 1.25e-04 | 2.95e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07175 | NA | NA | Up | Columella_Up |
| AT1G07290 | Columella | 36.40 | 29.40 | 11.70 | 16.80 | 20.80 | 35.20 | 0.1790 | 0.1620 | ⋯ | 21.50 | 3.56e-06 | 1.91e-04 | 4.00e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | GONST2 | NA | NA | Up | Columella_Up |
| AT1G07930 | Columella | 39.60 | 49.60 | 69.30 | 81.60 | 49.30 | 47.80 | 0.2640 | 0.2660 | ⋯ | 13.20 | 2.84e-04 | 7.14e-03 | 8.47e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | A1 | NA | NA | Down | Columella_Down |
| AT1G08310 | Columella | 7.25 | 11.10 | 9.20 | 2.96 | 16.80 | 8.53 | 0.0525 | 0.0704 | ⋯ | 10.50 | 1.17e-03 | 2.16e-02 | 2.26e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G08310 | NA | NA | Up | Columella_Up |
| AT1G08500 | Columella | 35.70 | 19.10 | 11.90 | 9.22 | 14.10 | 19.80 | 0.2110 | 0.1480 | ⋯ | 9.23 | 2.38e-03 | 3.72e-02 | 3.67e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ENODL18 | NA | NA | Up | Columella_Up |
| AT1G08890 | Columella | 11.70 | 13.90 | 5.05 | 2.63 | 8.57 | 13.50 | 0.0827 | 0.1050 | ⋯ | 19.90 | 8.27e-06 | 3.88e-04 | 7.02e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | SUGTL4 | NA | NA | Up | Columella_Up |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋱ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AT2G17660 | Pericycle | 0.982 | 1.4700 | 17.000 | 15.700 | 4.6400 | 2.700 | 0.02800 | 0.03160 | ⋯ | 55.1 | 5.99e-05 | 0.0317 | 0.002840 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G17660 | NA | NA | Down | Pericycle_Down |
| AT2G18620 | Pericycle | 1.720 | 1.9400 | 11.100 | 11.600 | 2.9100 | 3.470 | 0.04900 | 0.04580 | ⋯ | 53.9 | 6.52e-05 | 0.0327 | 0.003030 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G18620 | NA | NA | Down | Pericycle_Down |
| AT2G26910 | Pericycle | 3.680 | 2.3500 | 10.900 | 8.450 | 1.9800 | 1.450 | 0.08390 | 0.06160 | ⋯ | 80.5 | 1.45e-05 | 0.0166 | 0.001030 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ABCG32 | NA | NA | Down | Pericycle_Down |
| AT2G33790 | Pericycle | 12.800 | 11.3000 | 59.400 | 38.700 | 20.2000 | 7.720 | 0.28000 | 0.19600 | ⋯ | 43.1 | 1.46e-04 | 0.0411 | 0.005280 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AGP30 | NA | NA | Down | Pericycle_Down |
| AT2G33860 | Pericycle | 2.210 | 1.7000 | 5.710 | 7.330 | 0.8650 | 1.740 | 0.06290 | 0.04420 | ⋯ | 41.2 | 1.71e-04 | 0.0435 | 0.005930 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ARF3 | ETT | Transcriptional factor B3 family protein / auxin-responsive factor AUX/IAA-like protein | Down | Pericycle_Down |
| AT2G36640 | Pericycle | 0.000 | 0.8820 | 6.640 | 10.400 | 1.1100 | 1.250 | 0.00000 | 0.01260 | ⋯ | 41.9 | 1.61e-04 | 0.0432 | 0.005700 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ECP63 | NA | NA | Down | Pericycle_Down |
| AT2G37540 | Pericycle | 28.500 | 20.9000 | 3.540 | 2.710 | 11.6000 | 18.500 | 0.28000 | 0.25400 | ⋯ | 47.8 | 1.00e-04 | 0.0386 | 0.004090 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G37540 | NA | NA | Up | Pericycle_Up |
| AT2G37870 | Pericycle | 0.982 | 5.5800 | 66.300 | 68.100 | 7.1700 | 5.880 | 0.02100 | 0.04270 | ⋯ | 60.2 | 4.32e-05 | 0.0294 | 0.002260 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G37870 | NA | NA | Down | Pericycle_Down |
| AT2G38530 | Pericycle | 133.000 | 198.0000 | 110.000 | 84.100 | 326.0000 | 280.000 | 0.19600 | 0.22700 | ⋯ | 39.7 | 1.95e-04 | 0.0458 | 0.006530 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | LTP2 | NA | NA | Up | Pericycle_Up |
| AT2G39681 | Pericycle | 10.300 | 8.8800 | 4.720 | 3.750 | 14.3000 | 13.800 | 0.18900 | 0.14100 | ⋯ | 57.3 | 5.19e-05 | 0.0297 | 0.002550 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | TAS2 | NA | NA | Up | Pericycle_Up |
| AT2G39700 | Pericycle | 12.500 | 10.2000 | 8.690 | 4.940 | 35.5000 | 19.600 | 0.04900 | 0.05530 | ⋯ | 74.4 | 1.95e-05 | 0.0181 | 0.001270 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | EXPA4 | NA | NA | Up | Pericycle_Up |
| AT2G45050 | Pericycle | 3.930 | 2.8200 | 27.900 | 17.100 | 5.3800 | 4.150 | 0.09790 | 0.05850 | ⋯ | 95.0 | 7.65e-06 | 0.0142 | 0.000667 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | GATA2 | GATA2 | GATA transcription factor 2 | Down | Pericycle_Down |
| AT2G46400 | Pericycle | 28.200 | 50.7000 | 107.000 | 115.000 | 38.2000 | 37.100 | 0.16800 | 0.31300 | ⋯ | 37.6 | 2.36e-04 | 0.0497 | 0.007440 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | WRKY46 | WRKY46 | WRKY DNA-binding protein 46 | Down | Pericycle_Down |
| AT2G48010 | Pericycle | 5.400 | 3.7000 | 8.260 | 7.570 | 2.4100 | 2.320 | 0.13300 | 0.08060 | ⋯ | 39.4 | 2.01e-04 | 0.0465 | 0.006650 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RKF3 | NA | NA | Down | Pericycle_Down |
| AT4G01650 | Pericycle | 24.100 | 39.0000 | 11.400 | 9.640 | 41.6000 | 39.900 | 0.32200 | 0.39200 | ⋯ | 54.3 | 6.35e-05 | 0.0325 | 0.002970 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G01650 | NA | NA | Up | Pericycle_Up |
| AT4G04223 | Pericycle | 1.720 | 0.1760 | 4.780 | 4.220 | 0.0000 | 0.000 | 0.02800 | 0.00474 | ⋯ | 51.7 | 1.43e-04 | 0.0409 | 0.005210 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G04223 | NA | NA | Down | Pericycle_Down |
| AT4G11190 | Pericycle | 80.000 | 64.4000 | 197.000 | 204.000 | 91.7000 | 59.800 | 0.38500 | 0.27800 | ⋯ | 41.5 | 1.66e-04 | 0.0435 | 0.005820 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | DIR13 | NA | NA | Down | Pericycle_Down |
| AT4G11211 | Pericycle | 250.000 | 269.0000 | 96.700 | 84.300 | 338.0000 | 314.000 | 0.82500 | 0.83900 | ⋯ | 87.8 | 1.04e-05 | 0.0156 | 0.000819 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G11211 | NA | NA | Up | Pericycle_Up |
| AT4G12430 | Pericycle | 14.000 | 14.6000 | 5.090 | 4.620 | 12.3000 | 12.800 | 0.18200 | 0.18800 | ⋯ | 38.3 | 2.21e-04 | 0.0491 | 0.007120 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | TPPF | NA | NA | Up | Pericycle_Up |
| AT4G13860 | Pericycle | 8.100 | 10.6000 | 6.710 | 5.820 | 25.0000 | 18.600 | 0.15400 | 0.18500 | ⋯ | 50.9 | 8.01e-05 | 0.0357 | 0.003490 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G13860 | NA | NA | Up | Pericycle_Up |
| AT4G15920 | Pericycle | 12.000 | 13.5000 | 2.730 | 1.200 | 12.4000 | 16.700 | 0.23800 | 0.23400 | ⋯ | 58.8 | 4.73e-05 | 0.0294 | 0.002400 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | SWEET17 | NA | NA | Up | Pericycle_Up |
| AT4G16000 | Pericycle | 0.000 | 0.0588 | 3.910 | 3.670 | 0.0618 | 0.482 | 0.00000 | 0.00158 | ⋯ | 38.2 | 2.24e-04 | 0.0491 | 0.007180 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G16000 | NA | NA | Down | Pericycle_Down |
| AT4G16990 | Pericycle | 12.000 | 5.8800 | 0.124 | 0.159 | 4.5100 | 3.090 | 0.22400 | 0.12500 | ⋯ | 95.0 | 7.67e-06 | 0.0142 | 0.000668 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RLM3 | NA | NA | Up | Pericycle_Up |
| AT4G22214 | Pericycle | 16.400 | 12.2000 | 55.200 | 32.400 | 17.1000 | 14.100 | 0.31500 | 0.20100 | ⋯ | 45.5 | 1.20e-04 | 0.0386 | 0.004620 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G22214 | NA | NA | Down | Pericycle_Down |
| AT4G23450 | Pericycle | 11.800 | 15.3000 | 4.970 | 4.940 | 16.4000 | 17.800 | 0.18200 | 0.22300 | ⋯ | 63.3 | 3.59e-05 | 0.0270 | 0.001980 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AIRP1 | NA | NA | Up | Pericycle_Up |
| AT4G23680 | Pericycle | 0.245 | 0.7050 | 5.900 | 3.430 | 0.3090 | 0.386 | 0.00699 | 0.00632 | ⋯ | 50.3 | 8.35e-05 | 0.0365 | 0.003590 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G23680 | NA | NA | Down | Pericycle_Down |
| AT4G30660 | Pericycle | 8.840 | 10.2000 | 69.500 | 52.900 | 16.8000 | 23.400 | 0.22400 | 0.20400 | ⋯ | 41.1 | 1.73e-04 | 0.0435 | 0.005980 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G30660 | NA | NA | Down | Pericycle_Down |
| AT4G36880 | Pericycle | 24.100 | 23.6000 | 63.600 | 51.900 | 26.6000 | 23.000 | 0.32200 | 0.27600 | ⋯ | 37.5 | 2.39e-04 | 0.0500 | 0.007510 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | CP1 | NA | NA | Down | Pericycle_Down |
| AT4G39940 | Pericycle | 0.736 | 1.3500 | 20.100 | 16.000 | 5.5600 | 2.890 | 0.02100 | 0.02530 | ⋯ | 46.9 | 1.07e-04 | 0.0386 | 0.004290 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | APK2 | NA | NA | Down | Pericycle_Down |
| AT4G39950 | Pericycle | 2.700 | 2.5300 | 57.000 | 49.300 | 9.8300 | 5.110 | 0.02800 | 0.04900 | ⋯ | 124.0 | 2.71e-06 | 0.0102 | 0.000338 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | CYP79B2 | NA | NA | Down | Pericycle_Down |
sig_DE_fil
write.csv(sig_DE_fil, file = "../output/CVP/pCVP2_Citrine_celltype_EdgeR_q0.05_FC1.5_r_v_4_20240429.csv")
| gene | cluster_id | sc_130.cpm | sc_134.cpm | sc_131.cpm | sc_135.cpm | sc_132.cpm | sc_136.cpm | sc_130.frq | sc_134.frq | ⋯ | F | p_val | p_adj.loc | p_adj.glb | contrast | Name | TF_Name | Description | up_dn_label | clust_up_dn |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | ⋯ | <dbl> | <dbl> | <dbl> | <dbl> | <chr> | <chr> | <chr> | <chr> | <chr> | <chr> |
| AT1G01240 | Columella | 31.90 | 25.20 | 15.30 | 14.20 | 23.00 | 30.00 | 0.2090 | 0.1800 | ⋯ | 15.40 | 8.59e-05 | 2.69e-03 | 3.66e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01240 | NA | NA | Up | Columella_Up |
| AT1G01580 | Columella | 41.20 | 32.80 | 15.20 | 18.10 | 35.50 | 32.60 | 0.2500 | 0.2160 | ⋯ | 26.50 | 2.70e-07 | 2.02e-05 | 7.79e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | FRO2 | NA | NA | Up | Columella_Up |
| AT1G01620 | Columella | 623.00 | 348.00 | 256.00 | 189.00 | 287.00 | 386.00 | 0.9340 | 0.8040 | ⋯ | 21.40 | 3.71e-06 | 1.97e-04 | 4.11e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | PIP1-3 | NA | NA | Up | Columella_Up |
| AT1G01640 | Columella | 10.70 | 10.50 | 3.07 | 6.58 | 12.20 | 7.97 | 0.0626 | 0.0687 | ⋯ | 12.30 | 4.50e-04 | 1.02e-02 | 1.17e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01640 | AT1G01640 | BTB/POZ domain-containing protein | Up | Columella_Up |
| AT1G01725 | Columella | 14.90 | 16.20 | 4.87 | 4.28 | 16.20 | 18.70 | 0.1030 | 0.1190 | ⋯ | 43.00 | 5.57e-11 | 9.57e-09 | 7.61e-08 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G01725 | NA | NA | Up | Columella_Up |
| AT1G02430 | Columella | 8.99 | 7.98 | 5.23 | 3.29 | 6.73 | 11.70 | 0.0648 | 0.0619 | ⋯ | 10.70 | 1.10e-03 | 2.06e-02 | 2.17e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ATARFD1B | NA | NA | Up | Columella_Up |
| AT1G02610 | Columella | 23.10 | 23.30 | 13.50 | 10.90 | 23.60 | 22.60 | 0.1450 | 0.1580 | ⋯ | 15.30 | 9.08e-05 | 2.81e-03 | 3.80e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G02610 | NA | NA | Up | Columella_Up |
| AT1G02860 | Columella | 70.90 | 71.80 | 51.40 | 38.50 | 77.40 | 70.30 | 0.3270 | 0.3280 | ⋯ | 16.50 | 4.82e-05 | 1.66e-03 | 2.43e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | BAH1 | NA | NA | Up | Columella_Up |
| AT1G02870 | Columella | 6.24 | 17.00 | 18.60 | 22.70 | 11.90 | 11.70 | 0.0425 | 0.0945 | ⋯ | 11.60 | 6.48e-04 | 1.36e-02 | 1.51e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G02870 | NA | NA | Down | Columella_Down |
| AT1G03030 | Columella | 19.70 | 19.70 | 13.20 | 14.80 | 19.90 | 24.90 | 0.1400 | 0.1370 | ⋯ | 8.76 | 3.07e-03 | 4.53e-02 | 4.38e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03030 | NA | NA | Up | Columella_Up |
| AT1G03200 | Columella | 14.20 | 13.40 | 4.69 | 6.91 | 12.90 | 13.50 | 0.0883 | 0.1030 | ⋯ | 17.30 | 3.15e-05 | 1.17e-03 | 1.79e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03200 | NA | NA | Up | Columella_Up |
| AT1G03850 | Columella | 58.40 | 53.40 | 42.00 | 38.50 | 62.10 | 88.80 | 0.2980 | 0.2770 | ⋯ | 25.60 | 4.23e-07 | 2.97e-05 | 1.05e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G03850 | NA | NA | Up | Columella_Up |
| AT1G03870 | Columella | 221.00 | 105.00 | 95.20 | 53.00 | 117.00 | 139.00 | 0.6830 | 0.4900 | ⋯ | 29.50 | 5.65e-08 | 4.88e-06 | 2.58e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | FLA9 | NA | NA | Up | Columella_Up |
| AT1G04100 | Columella | 22.20 | 24.40 | 36.10 | 35.60 | 24.50 | 21.10 | 0.1490 | 0.1600 | ⋯ | 11.00 | 9.21e-04 | 1.80e-02 | 1.93e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | IAA10 | IAA10 | indoleacetic acid-induced protein 10 | Down | Columella_Down |
| AT1G04180 | Columella | 20.30 | 20.20 | 6.13 | 9.22 | 11.00 | 10.00 | 0.0782 | 0.0893 | ⋯ | 15.10 | 1.03e-04 | 1.43e-02 | 3.56e-02 | pCVP2_BRI1_Citrine_bri1_T-WT | YUC9 | NA | NA | Down | Columella_Down |
| AT1G04280 | Columella | 14.10 | 13.40 | 5.23 | 4.61 | 14.40 | 13.40 | 0.0883 | 0.1010 | ⋯ | 24.70 | 6.79e-07 | 4.48e-05 | 1.45e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G04280 | NA | NA | Up | Columella_Up |
| AT1G04870 | Columella | 2.18 | 2.94 | 8.30 | 12.20 | 3.37 | 4.08 | 0.0168 | 0.0223 | ⋯ | 16.70 | 4.28e-05 | 1.51e-03 | 2.24e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | PRMT10 | NA | NA | Down | Columella_Down |
| AT1G05680 | Columella | 1080.00 | 1030.00 | 730.00 | 738.00 | 1180.00 | 1110.00 | 0.7550 | 0.6740 | ⋯ | 29.30 | 6.39e-08 | 5.49e-06 | 2.82e-05 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | UGT74E2 | NA | NA | Up | Columella_Up |
| AT1G05840 | Columella | 7.54 | 9.24 | 3.25 | 5.93 | 10.40 | 7.23 | 0.0547 | 0.0739 | ⋯ | 8.60 | 3.36e-03 | 4.86e-02 | 4.65e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G05840 | NA | NA | Up | Columella_Up |
| AT1G06090 | Columella | 81.10 | 124.00 | 88.70 | 37.50 | 144.00 | 79.90 | 0.2020 | 0.2290 | ⋯ | 24.50 | 7.40e-07 | 4.81e-05 | 1.52e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G06090 | NA | NA | Up | Columella_Up |
| AT1G06330 | Columella | 54.40 | 46.40 | 20.20 | 21.10 | 34.30 | 41.70 | 0.2800 | 0.2440 | ⋯ | 20.80 | 5.25e-06 | 2.64e-04 | 5.20e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G06330 | NA | NA | Up | Columella_Up |
| AT1G07030 | Columella | 71.80 | 58.00 | 44.70 | 43.80 | 65.80 | 66.80 | 0.4010 | 0.3570 | ⋯ | 11.20 | 8.39e-04 | 1.67e-02 | 1.81e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07030 | NA | NA | Up | Columella_Up |
| AT1G07070 | Columella | 5.22 | 9.03 | 17.00 | 21.70 | 10.70 | 11.70 | 0.0402 | 0.0704 | ⋯ | 9.73 | 1.81e-03 | 3.02e-02 | 3.06e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RPL35AA | NA | NA | Down | Columella_Down |
| AT1G07160 | Columella | 209.00 | 149.00 | 113.00 | 116.00 | 179.00 | 253.00 | 0.5520 | 0.4600 | ⋯ | 36.70 | 1.38e-09 | 1.76e-07 | 1.31e-06 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07160 | NA | NA | Up | Columella_Up |
| AT1G07175 | Columella | 158.00 | 134.00 | 81.30 | 100.00 | 141.00 | 162.00 | 0.4590 | 0.4020 | ⋯ | 22.40 | 2.21e-06 | 1.25e-04 | 2.95e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G07175 | NA | NA | Up | Columella_Up |
| AT1G07290 | Columella | 36.40 | 29.40 | 11.70 | 16.80 | 20.80 | 35.20 | 0.1790 | 0.1620 | ⋯ | 21.50 | 3.56e-06 | 1.91e-04 | 4.00e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | GONST2 | NA | NA | Up | Columella_Up |
| AT1G07930 | Columella | 39.60 | 49.60 | 69.30 | 81.60 | 49.30 | 47.80 | 0.2640 | 0.2660 | ⋯ | 13.20 | 2.84e-04 | 7.14e-03 | 8.47e-03 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | A1 | NA | NA | Down | Columella_Down |
| AT1G08310 | Columella | 7.25 | 11.10 | 9.20 | 2.96 | 16.80 | 8.53 | 0.0525 | 0.0704 | ⋯ | 10.50 | 1.17e-03 | 2.16e-02 | 2.26e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT1G08310 | NA | NA | Up | Columella_Up |
| AT1G08500 | Columella | 35.70 | 19.10 | 11.90 | 9.22 | 14.10 | 19.80 | 0.2110 | 0.1480 | ⋯ | 9.23 | 2.38e-03 | 3.72e-02 | 3.67e-02 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ENODL18 | NA | NA | Up | Columella_Up |
| AT1G08890 | Columella | 11.70 | 13.90 | 5.05 | 2.63 | 8.57 | 13.50 | 0.0827 | 0.1050 | ⋯ | 19.90 | 8.27e-06 | 3.88e-04 | 7.02e-04 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | SUGTL4 | NA | NA | Up | Columella_Up |
| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋱ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
| AT2G17660 | Pericycle | 0.982 | 1.4700 | 17.000 | 15.700 | 4.6400 | 2.700 | 0.02800 | 0.03160 | ⋯ | 55.1 | 5.99e-05 | 0.0317 | 0.002840 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G17660 | NA | NA | Down | Pericycle_Down |
| AT2G18620 | Pericycle | 1.720 | 1.9400 | 11.100 | 11.600 | 2.9100 | 3.470 | 0.04900 | 0.04580 | ⋯ | 53.9 | 6.52e-05 | 0.0327 | 0.003030 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G18620 | NA | NA | Down | Pericycle_Down |
| AT2G26910 | Pericycle | 3.680 | 2.3500 | 10.900 | 8.450 | 1.9800 | 1.450 | 0.08390 | 0.06160 | ⋯ | 80.5 | 1.45e-05 | 0.0166 | 0.001030 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ABCG32 | NA | NA | Down | Pericycle_Down |
| AT2G33790 | Pericycle | 12.800 | 11.3000 | 59.400 | 38.700 | 20.2000 | 7.720 | 0.28000 | 0.19600 | ⋯ | 43.1 | 1.46e-04 | 0.0411 | 0.005280 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AGP30 | NA | NA | Down | Pericycle_Down |
| AT2G33860 | Pericycle | 2.210 | 1.7000 | 5.710 | 7.330 | 0.8650 | 1.740 | 0.06290 | 0.04420 | ⋯ | 41.2 | 1.71e-04 | 0.0435 | 0.005930 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ARF3 | ETT | Transcriptional factor B3 family protein / auxin-responsive factor AUX/IAA-like protein | Down | Pericycle_Down |
| AT2G36640 | Pericycle | 0.000 | 0.8820 | 6.640 | 10.400 | 1.1100 | 1.250 | 0.00000 | 0.01260 | ⋯ | 41.9 | 1.61e-04 | 0.0432 | 0.005700 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | ECP63 | NA | NA | Down | Pericycle_Down |
| AT2G37540 | Pericycle | 28.500 | 20.9000 | 3.540 | 2.710 | 11.6000 | 18.500 | 0.28000 | 0.25400 | ⋯ | 47.8 | 1.00e-04 | 0.0386 | 0.004090 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G37540 | NA | NA | Up | Pericycle_Up |
| AT2G37870 | Pericycle | 0.982 | 5.5800 | 66.300 | 68.100 | 7.1700 | 5.880 | 0.02100 | 0.04270 | ⋯ | 60.2 | 4.32e-05 | 0.0294 | 0.002260 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT2G37870 | NA | NA | Down | Pericycle_Down |
| AT2G38530 | Pericycle | 133.000 | 198.0000 | 110.000 | 84.100 | 326.0000 | 280.000 | 0.19600 | 0.22700 | ⋯ | 39.7 | 1.95e-04 | 0.0458 | 0.006530 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | LTP2 | NA | NA | Up | Pericycle_Up |
| AT2G39681 | Pericycle | 10.300 | 8.8800 | 4.720 | 3.750 | 14.3000 | 13.800 | 0.18900 | 0.14100 | ⋯ | 57.3 | 5.19e-05 | 0.0297 | 0.002550 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | TAS2 | NA | NA | Up | Pericycle_Up |
| AT2G39700 | Pericycle | 12.500 | 10.2000 | 8.690 | 4.940 | 35.5000 | 19.600 | 0.04900 | 0.05530 | ⋯ | 74.4 | 1.95e-05 | 0.0181 | 0.001270 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | EXPA4 | NA | NA | Up | Pericycle_Up |
| AT2G45050 | Pericycle | 3.930 | 2.8200 | 27.900 | 17.100 | 5.3800 | 4.150 | 0.09790 | 0.05850 | ⋯ | 95.0 | 7.65e-06 | 0.0142 | 0.000667 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | GATA2 | GATA2 | GATA transcription factor 2 | Down | Pericycle_Down |
| AT2G46400 | Pericycle | 28.200 | 50.7000 | 107.000 | 115.000 | 38.2000 | 37.100 | 0.16800 | 0.31300 | ⋯ | 37.6 | 2.36e-04 | 0.0497 | 0.007440 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | WRKY46 | WRKY46 | WRKY DNA-binding protein 46 | Down | Pericycle_Down |
| AT2G48010 | Pericycle | 5.400 | 3.7000 | 8.260 | 7.570 | 2.4100 | 2.320 | 0.13300 | 0.08060 | ⋯ | 39.4 | 2.01e-04 | 0.0465 | 0.006650 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RKF3 | NA | NA | Down | Pericycle_Down |
| AT4G01650 | Pericycle | 24.100 | 39.0000 | 11.400 | 9.640 | 41.6000 | 39.900 | 0.32200 | 0.39200 | ⋯ | 54.3 | 6.35e-05 | 0.0325 | 0.002970 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G01650 | NA | NA | Up | Pericycle_Up |
| AT4G04223 | Pericycle | 1.720 | 0.1760 | 4.780 | 4.220 | 0.0000 | 0.000 | 0.02800 | 0.00474 | ⋯ | 51.7 | 1.43e-04 | 0.0409 | 0.005210 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G04223 | NA | NA | Down | Pericycle_Down |
| AT4G11190 | Pericycle | 80.000 | 64.4000 | 197.000 | 204.000 | 91.7000 | 59.800 | 0.38500 | 0.27800 | ⋯ | 41.5 | 1.66e-04 | 0.0435 | 0.005820 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | DIR13 | NA | NA | Down | Pericycle_Down |
| AT4G11211 | Pericycle | 250.000 | 269.0000 | 96.700 | 84.300 | 338.0000 | 314.000 | 0.82500 | 0.83900 | ⋯ | 87.8 | 1.04e-05 | 0.0156 | 0.000819 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G11211 | NA | NA | Up | Pericycle_Up |
| AT4G12430 | Pericycle | 14.000 | 14.6000 | 5.090 | 4.620 | 12.3000 | 12.800 | 0.18200 | 0.18800 | ⋯ | 38.3 | 2.21e-04 | 0.0491 | 0.007120 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | TPPF | NA | NA | Up | Pericycle_Up |
| AT4G13860 | Pericycle | 8.100 | 10.6000 | 6.710 | 5.820 | 25.0000 | 18.600 | 0.15400 | 0.18500 | ⋯ | 50.9 | 8.01e-05 | 0.0357 | 0.003490 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G13860 | NA | NA | Up | Pericycle_Up |
| AT4G15920 | Pericycle | 12.000 | 13.5000 | 2.730 | 1.200 | 12.4000 | 16.700 | 0.23800 | 0.23400 | ⋯ | 58.8 | 4.73e-05 | 0.0294 | 0.002400 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | SWEET17 | NA | NA | Up | Pericycle_Up |
| AT4G16000 | Pericycle | 0.000 | 0.0588 | 3.910 | 3.670 | 0.0618 | 0.482 | 0.00000 | 0.00158 | ⋯ | 38.2 | 2.24e-04 | 0.0491 | 0.007180 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G16000 | NA | NA | Down | Pericycle_Down |
| AT4G16990 | Pericycle | 12.000 | 5.8800 | 0.124 | 0.159 | 4.5100 | 3.090 | 0.22400 | 0.12500 | ⋯ | 95.0 | 7.67e-06 | 0.0142 | 0.000668 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | RLM3 | NA | NA | Up | Pericycle_Up |
| AT4G22214 | Pericycle | 16.400 | 12.2000 | 55.200 | 32.400 | 17.1000 | 14.100 | 0.31500 | 0.20100 | ⋯ | 45.5 | 1.20e-04 | 0.0386 | 0.004620 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G22214 | NA | NA | Down | Pericycle_Down |
| AT4G23450 | Pericycle | 11.800 | 15.3000 | 4.970 | 4.940 | 16.4000 | 17.800 | 0.18200 | 0.22300 | ⋯ | 63.3 | 3.59e-05 | 0.0270 | 0.001980 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AIRP1 | NA | NA | Up | Pericycle_Up |
| AT4G23680 | Pericycle | 0.245 | 0.7050 | 5.900 | 3.430 | 0.3090 | 0.386 | 0.00699 | 0.00632 | ⋯ | 50.3 | 8.35e-05 | 0.0365 | 0.003590 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G23680 | NA | NA | Down | Pericycle_Down |
| AT4G30660 | Pericycle | 8.840 | 10.2000 | 69.500 | 52.900 | 16.8000 | 23.400 | 0.22400 | 0.20400 | ⋯ | 41.1 | 1.73e-04 | 0.0435 | 0.005980 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | AT4G30660 | NA | NA | Down | Pericycle_Down |
| AT4G36880 | Pericycle | 24.100 | 23.6000 | 63.600 | 51.900 | 26.6000 | 23.000 | 0.32200 | 0.27600 | ⋯ | 37.5 | 2.39e-04 | 0.0500 | 0.007510 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | CP1 | NA | NA | Down | Pericycle_Down |
| AT4G39940 | Pericycle | 0.736 | 1.3500 | 20.100 | 16.000 | 5.5600 | 2.890 | 0.02100 | 0.02530 | ⋯ | 46.9 | 1.07e-04 | 0.0386 | 0.004290 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | APK2 | NA | NA | Down | Pericycle_Down |
| AT4G39950 | Pericycle | 2.700 | 2.5300 | 57.000 | 49.300 | 9.8300 | 5.110 | 0.02800 | 0.04900 | ⋯ | 124.0 | 2.71e-06 | 0.0102 | 0.000338 | pCVP2_BRI1_Citrine_bri1_T-bri1_T | CYP79B2 | NA | NA | Down | Pericycle_Down |
# add DE and up/dn to total list
sig_to_join <- sig_DE_fil %>%
mutate(clust_gene=paste(contrast, cluster_id, gene, sep="_")) %>%
select(clust_gene, up_dn_label, clust_up_dn)
all_bg <- mutate(all_bg, clust_gene=paste(contrast, cluster_id, gene, sep="_"))
all_bg <- left_join(all_bg, feature_names, by=c("gene"="AGI"))
all_bg$DE <- all_bg$clust_gene %in% sig_to_join$clust_gene
all_bg <- all_bg %>%
left_join(sig_to_join, by="clust_gene") %>%
arrange(all_bg, p_adj.loc)
write.csv(all_bg, file = "../output/CVP/all_genes_pCVP2_Citrine_celltype_EdgeR_q0.05_FC1.5_r_v_4_20240429.csv")
rc.integrated$geno <- factor(rc.integrated$geno,
levels=c("WT", "bri1_T", "pCVP2_BRI1_Citrine_bri1_T"))
options(repr.plot.width=16.5, repr.plot.height=6)
(Celltype_umap <- DimPlot(rc.integrated,
reduction = "umap",
group.by = "cell_type",
cols = color, split.by = 'geno',
ncol=3,
pt.size = 0.5))
ggsave("../output/CVP/Cell_type_umap_square.pdf", width=16.5, height=6)
options(repr.plot.width = 18, repr.plot.height = 6)
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="BRI1-mCitrine", split.by = "geno", order=T, max.cutoff = "q90", pt.size = 0.5)
ggsave("../output/CVP/BRI1-mCitrine_expression.pdf", width=18.3, height=6)
Warning message in FeaturePlot(rc.integrated, features = "BRI1-mCitrine", split.by = "geno", : “All cells have the same value (0) of BRI1-mCitrine.”
# expression of CVP2
options(repr.plot.width = 18, repr.plot.height = 6)
DefaultAssay(rc.integrated) <- "SCT"
# expression of the transgene
FeaturePlot(rc.integrated, features="AT1G05470", split.by = "geno", order=T, max.cutoff = "q90", pt.size = 0.5)
ggsave("../output/CVP/CVP2_AT1G05470_expression.pdf", width=18.3, height=6)